Before Vito killed Fanucci, Clemenza was sort of the leader of the Vito/Clemenza/Tessio crew. As Fanucci put it to Vito, "Your friend Clemenza understands these things".
However, notice how humbled and respectful Clemenza is in the presence of "Mr. Corleone" when he is introducing Hyman Roth?
Clemenza even takes off his hat when Vito and Genco come out to the garage.
